L. Van Meervelt

X‐ray and vibrational studies of 8‐aminoquinoline. Evidence for a three‐center hydrogen bond

The x-ray structure of 8-aminoquinoline indicates that one of the NH bonds of the NH2 group forms a three-center hydrogen bond, the major component being the intramolecular hydrogen bond and the minor component the intermolecular hydrogen bond. The IR and Raman spectra of 8-aminoquinoline and of its N-deuterated counterpart reflect the non-equivalence of the two NH(D) bonds and the weakness of the hydrogen bridge

Divergent pathways in the intramolecular diels-alder reaction of 2(1H)-pyrazinones substituted at the 3-position with a phenylalkyne containing side chain

Abstract 2(1H)-Pyrazinones bearing an X-(o-C6H4)-CC-R moiety (X = O or NH; R = H, Ph or TMS) at position 3 were subjected to intramolecular Diels-Alder reaction. For the ether compounds (X = O) cycloaddition-elimination occurred readily to produce either benzofuro[2,3-c]pyridin-1(2-H)-ones or benzofuro[2,3-b]pyridines. For the aniline derivatives (X = NH, R = H or TMS) thermolysis in acetic anhydride resulted in a similar product distribution of β-carbolinones and α-carbolines which, however, differed from that obtained previously in refluxing tetrahydronaphthalene. This result is explained by the cycloaddition proceeding from the aniline NH-acetylated precursor. However, the aniline derivatives with Ph as the acetylenic end group (X = NH, R = Ph) reacted via a divergent pathway to produce N-(2-oxopyrazin-3-yl)-2-Ph-substituted indoles.

DNA–Drug Refinement: a Comparison of the Programs NUCLSQ, PROLSQ, SHELXL93 and X‐PLOR, Using the Low‐Temperature d(TGATCA)–Nogalamycin Structure

In an earlier study [Smith, Davies, Dodson & Moore (1995). Biochemistry, 34, 415-425] the crystal structure of the d(TGATCA)-nogalamycin complex was determined to 1.8 A and refined with PROLSQ to R = 19.5% against 4767 reflections with F> 1sigma(F). A low-temperature crystallographic study on this complex has now been performed. Native data collection at liquid-nitrogen temperature (120 K) improved the resolution to 1.4 A. The structure has now been refined against these new diffraction data in the resolution range 8-1.4 A using NUCLSQ, PROLSQ, SHELXL93 and X-PLOR, in order to determine to what extent the resulting DNA conformation and associated solvent structure would differ and to examine the suitability of these programs for the refinement of oligonucleotide structures. With the advent of more DNA-protein structure determinations, it is of interest to see how well the protein-refinement packages, PROLSQ and X-PLOR, and the small-molecule program, SHELXL93, are able to accommodate DNA. Comparisons are made between the dictionaries, weights and restraints used and the final models obtained from each program. Although the final R values, using all data in the resolution range 8.0-1.4 A, from PROLSQ (22.8%), SHELXL93 (R1 =21.7% after isotropic refinement) and X-PLOR (24.4%) are higher than the R value from the NUCLSQ refinement (21.2%), the root-mean-square deviations between the four final models are very small. Using this high-quality 8.0-1.4 A data set neither the dictionary nor the refinement program leave an imprint on the final fully refined complex. Likewise, the helical parameters and backbone conformation including sugar-puckering modes are not influenced by the refinement procedure used. Although a different number of water molecules is found in each refinement, varying from 62 (X-PLOR) to 86 (NUCLSQ), the first hydration sphere is well conserved in all four models.

X-ray and IR studies of N-(tert-butoxycarbonyl)-l-alanine. Comparison with N-(tert-butoxycarbonyl)glycine

Abstract The X-ray structure of the amino acid N-(tert- butoxycarbonyl)- l -alanine (B- l -ALA) has been determined and its IR spectrum interpreted. The molecules are held together by intermolecular OH···O hydrogen bonds between the carboxyl groups which are in a cyclic arrangement. Weaker hydrogen bonds are formed between the NH and carbonyl urethane groups. The IR spectrum of B- l -ALA differs markedly from that of N -( tert -butoxycarbonyl)glycine. The results are discussed as a function of the hydrogen bonding pattern of the two molecules and the higher asymmetry of the crystal packing in the glycine derivative.

TO WOBBLE OR NOT TO WOBBLE: MODIFIED BASES INCORPORATED INTO DNA

Abstract The ambivalent base analogue P was incorporated in the d(CGCGPG) hexamer to investigate the G.P base pair geometry by X-ray diffraction. Both Watson-Crick and wobble geometries have been found for the crystallographic independent G.P base pairs.

6-(3,5-Di-O-acetyl-β-d-2-deoxyribofuranosyl)-3,4-dihydro-8H-pyrimido[4,5-c][1,2]oxazin-7(6H)-one

The title compound, C 15 H 19 N 3 O 7 (P), crystallizes with two molecules in the asymmetric unit which differ in sugar and oxazino ring puckering ; both occur as the imino tautomer and form P :P wobble base pairs.

Absolute configuration of 3-acetylbetulinic acid

The absolute configuration of 3-acetoxybetulinic acid is determined by single crystal X-ray diffraction.

Ethyl 2-(2,3-dioxoindolin-1-yl)acetate

The mol-ecular structure of the title compound, C12H11NO4, at 100 (2) K is characterized by a planar indole ring system, containing a long C - C bond in the 1,2-diketone unit.

1,5-Anhydro-2,3-dideoxy-2-(guanin-9-yl)-D-arabino-hexitol

The molecular shape of the title compound, C 11 H 15 N 5 O 4 , in the crystalline state is characterized by the chair conformation of the sugar moiety and the axial position of the guanine substituent.

Molecular and Crystal Structure of d(CGCGmo4CG): N4−Methoxy-cytosineguanine Base Pairs in Z-DNA

The base analogue N4-methoxycytosine (mo4C) is ambivalent in its hydrogen-bonding potential, since it forms stable base-pairs with both adenine and guanine in oligomer duplexes. To investigate the base-pair geometry, the structure of d(CGCGmo4CG) has been determined by single-crystal X-ray diffraction techniques. The d(CGCGmo4CG)2 crystallized in a left-handed double helical structure (Z-type). Refinement using 2559 reflections between 10 and 1.7 A converged with a final R = 0.181 (Rw = 0.130) including 68 solvent molecules. The orthorhombic crystals are in the space group P2(1)2(1)2(1), with cell dimensions a = 18.17 A, b = 30.36 A, c = 43.93 A. The mo4C.G base-pair is of the wobble type, with mo4C in the imino form, and the methoxy group in the syn configuration.